I ran MD simulation of a complex protein eg. gp120 and BMS-488043 using AMBER12. I successfully passed from all steps given in the amber toturial, but when I upload the complex protein in the xleap universe editor, it closed automatically. Kindly help me if you know why this error occured.
sir, i still recieved an error but now this type of error is in generation of prmtop and inpcrd files of ligand these files are generated but they are empty file nothing was there.And another problem is that there is an alphabet M^ this is present in protein complex.pdb text form..why this is present in text form when complex open in linux and not present when open in moe. Kindly help me if anyone knows......
sir , you have modified the pdb file but still there is an error so why it is.....kindly help me
This problem usually occurs due to manual fiddling changes of pdb files.
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I modified your pdb file.Let me informed if any problem comes up.
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